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HISAT2-BUILD-S(1) User Commands HISAT2-BUILD-S(1)


hisat2-build-s - HISAT2 indexer, small index binary


hisat2-build [options]* <reference_in> <ht2_index_base>


HISAT2 version 2.2.1 by Daehwan Kim (,

comma-separated list of files with ref sequences
write ht2 data to files with this dir/basename


reference sequences given on cmd line (as <reference_in>)
disable automatic -p/--bmax/--dcv memory-fitting
number of threads
max bucket sz for blockwise suffix-array builder
max bucket sz as divisor of ref len (default: 4)
diff-cover period for blockwise (default: 1024)
disable diff-cover (algorithm becomes quadratic)
don't build .3/.4.ht2 (packed reference) portion
just build .3/.4.ht2 (packed reference) portion
SA is sampled every 2^offRate BWT chars (default: 5)
# of chars consumed in initial lookup (default: 10)
SA (local) is sampled every 2^offRate BWT chars (default: 3)
# of chars consumed in initial lookup in a local index (default: 6)
SNP file name
haplotype file name
Splice site file name
Exon file name
Repeat reference file name
Repeat information file name
Repeat snp file name
Repeat haplotype file name
seed for random number generator
disable verbose output (for debugging)
print detailed description of tool and its options
print this usage message
print version information and quit

64-bit Built on Debian 05 August 2021 Compiler: gcc version 10.2.1 20210110 (Debian 10.2.1-6) Options: -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

August 2021 hisat2-build-s version 2.2.1